Besides that there's also an unexplainable appearance in one of the late eps, 21 ("Being Meltdown") I think. Kurisu and Okabe is sitting in a stair, talking, and then the scene quickly flickers to the purple-hair chick.

I thought so too. Naturally, she looks identical to Kurisu except for the hair part.

But the one piece of the puzzle that doesn't fit together is that scene in ep 21. We get a quick flash to that chick, and the lightning looks normal. (And this is actually just the only time when the chick is "awake").

It just doesn't fit. Maybe it alludes to some parallel version of Kurisu.

While I'm at it, Okabes dream from 65 B.C. is also something that doesn't come together straight away.